Adding methods to get fitted, residual, and new predictions from lava…

[jebyrnes]

Adding methods to get fitted, residual, and new predictions from lavaan, pending them being added to the main package. I had a hard time compiling the package with devtools given a few of the scripts. Perhaps could you put a package build file in the master branch? If this all goes through, I'll add my lavSpatialCorrect script back shortly.

[TDJorgensen]

Hi Jarrett,

Thanks for the contribution! I really think this is something important missing from lavaan, and clearly there are many who would like this functionality. I just saw David Kaplan post about this on the lavaan board, and I reminded me I had not gotten back to you yet. I am slammed with teaching and won't have time to actively maintain semTools until February (lots of changes to make then!), but I linked him to your source code on your github fork.

In the meantime, I have added a source tarball to the /builds subdirectory as you requested. Hope it helps.

Terrence

[TDJorgensen]

Hi Jarrett,

I'm still hoping to have time to include this in the next version of semTools. Hopefully when lavaan goes to CRAN in about a month.

Can you check whether your code still works with the latest development version of lavaan?

Also, the NAMESPACE file seems to indicate we are importing a stats() function from the lavaan package, but there is none. This is because the following roxygen2 comment appears above each function:

#' @importFrom lavaan stats

I think you intend to import particular functions from these packages instead. Can you list them explicitly and update the pull request?

#' @importFrom lavaan func1 func2
#' @importFrom stats func1 func2

Thanks!

[drakesiard]

Hello,
I'm not sure of the etiquette involved, so please let me know if I'm doing something wrong by jumping in. I've rebased @jebyrnes's patch onto the most recent master and fixed up the roxygen2 comments (and function imports more generally); it's available here. I've also added a separate commit with some lint picking and general tidy up of examples, but that can be a separate PR if you'd like.

Would you like me to create a PR from my branch onto simsem:master, or onto jebyrnes:master? Also, please let me know if there is anything else you would need to make my changes package-worthy.

Thanks!

[TDJorgensen]

Thanks for picking this up again, Drake. I would just accept a pull request from your own clone with the additional commit(s), and add you both to the DESCRIPTION file. I just had a baby, so my time is obviously limited, but before accepting a PR, I would want to make sure that informative errors are issued for situations (possibly) not accommodated by these functions, and check whether the output is consistent under different lavInspect(fit, "options").

• categorical endogenous variables (or are they? If so, are expected probabilities or probits returned, and could this be controlled by a type = c("link", "response") argument like predict.glm() has?)
• multilevel models (check using lavInspect(fit, "nlevels") == 1L)
• works whether fixed.x=TRUE (default) or FALSE
• works when conditional.x=TRUE (default in models with categorical endogenous variables)?

I think the calculations would be more complicated when conditional.x=TRUE, so no need to implement these methods for that option; just a check to warn users that they should set it FALSE in order to use the methods.

Finally, perhaps the function names could be extended to fitted_ov_lavaan() and such, to make sure users understand these functions are designed only for observed-variable models.

[drakesiard]

Thanks for the feedback. I'll look to make those changes and submit a new PR when I'm done.

p.s. Congratulations, by the way!

[TDJorgensen]

Hi Drake, I just made some updates, some of which are related to R 4.0, so please make sure you are working with that version when you test your new PR (also use the latest lavaan 0.6-6).

FYI, I am about to submit a new semTools to CRAN. No rush on your new PR; I can include it in the next version.

[drakesiard]

Thanks for letting me know. Exam season is here, so I probably won't be able to update and finish the changes before mid-June.